Changes in Soil Microbial Activity and Community Composition as a Result of Selected Agricultural Practices

For a constantly growing human population, healthy and productive soil is critical for sustainable delivery of agricultural products. The soil microorganisms play a crucial role in soil structure and functioning. They are responsible for soil formation, ecosystem biogeochemistry, cycling of nutrients and degradation of plant residues and xenobiotics. Certain agricultural treatments, such as fertilizers and pesticides applications, crop rotation, or soil amendment addition, influence the composition, abundance and function of bacteria and fungi in the soil ecosystems. Some of these practices have rather negative effects;others can help soil microorganisms by creating a friendlier habitat or providing nutrients. The changes in microbial community structure cannot be fully captured with traditional methods that are limited only to culturable organisms, which represent less than 1% of the whole population. The use of new molecular techniques such as metagenomics offers the possibility to better understand how agriculture affects soil microbiota. Therefore, the main goal of this review is to discuss how common farming practices influence microbial activity in the soil, with a special focus on pesticides, fertilizers, heavy metals and crop rotation. Furthermore, potential practices to mitigate the negative effects of some treatments are suggested and treatments that can beneficially influence soil microbiota are pointed out. Finally, application of metagenomics technique in agriculture and perspectives of developing efficient molecular tools in order to assess soil condition in the context of microbial activities are underlined.

Combined Effects of Nutrient and Pesticide Management on Soil Microbial Activity in Hybrid Rice Double Annual Cropping System

Combined effects on soil microbial activity of nutrient and pesticide management in hybrid rice double annual cropping system were studied. Results of field experiment demonstrated significant changes in soil microbial biomass phospholipid contents, abundance of heterotrophic bacteria and proteolytic bacteria, electron transport system (ETS)/dehydrogenase activity, soil protein contents under different management practices and at various growth stages. Marked depletions in the soil microbial biomass phospholipid contents were found with the advancement of crop growth stages, while the incorporation of fertilizers and/or pesticides also induced slight changes, and the lowest microbial biomass phospholipid content was found with pesticides application alone. A decline in the bacterial abundance of heterotrophic bacteria and proteolytic bacteria was observed during the continuance of crop growth, while the lowest abundance of heterotrophic bacteria and proteolytic bacteria was found with pesticides application alone, which coincided with the decline of soil microbial biomass. A consistent increase in the electron transport system activity was measured during the different crop growth stages of rice. The use of fertilizers (NPK) alone or combined with pesticides increased it, while a decline was noticed with pesticides application alone as compared with the control. The soil protein content was found to be relatively stable with fertilizers and/or pesticides application at various growth stages in both crops undertaken, but notable changes were detected at different growth stages.

Lindane Degradation and Effects on Soil Microbial Activity

The degradation of U-14C-lindane in two Egyptian soils was determined in a three-month laboratory incubation. Lindane mineralization was slow and limited in both soils. Evolution of 14CO2 increased with time but only reached 3. 5 to 5. 5 % of the initial 14C-concentration within 90 days. At that time both soils contained about 88 % of the applied radiocarbon; 33 % to 37% of the initial dose was unextractable and assumed bound to the soils. The methanol-ex-tractable 14C primarily contained lindane with traces of minor metabolites. Radiorespirometry was used to eva1uate the effect of lindane on soil microbial activity. Low concentrations of the insecticide initially supressed 14CO2 evolution from U-14C-glucose and microbial activity was significantly inhibited by 10 mg lindane/kg soil.

Methyl-β-cyclodextrin enhanced biodegradation of polycyclic aromatic hydrocarbons and associated microbial activity in contaminated soil

The contamination of soils by polycyclic aromatic hydrocarbons （PAHs） is a widespread environmental problem and the remediation of PAHs from these areas has been a major concern. The effectiveness of many in situ bioremediation systems may be constrained by low contaminant bioavailability due to limited aqueous solubility or a large magnitude of sorption. The objective of this research was to evaluate the effect of methyl-β-cyclodextrin （MCD） on bioaugmentation by Paracoccus sp. strain HPD-2 of an aged PAH-contaminated soil. When 10% （W/W） MCD amendment was combined with bioaugmentation by the PAH-degrading bacterium Paracoccus sp. strain HPD-2, the percentage degradation of total PAHs was significantly enhanced up to 34.8%. Higher counts of culturable PAH- degrading bacteria and higher soil dehydrogenase and soil polyphenol oxidase activities were observed in 10% （W/W） MCD-assisted bioaugmentation soil. This MCD-assisted bioaugmentation strategy showed significant increases （p 〈 0.05） in the average well color development （AWCD） obtained by the BIOLOG Eco plate assay, Shannon-Weaver index （H） and Simpson index （λ） compared with the controls, implying that this strategy at least partially restored the microbiological functioning of the PAH-contaminated soil. The results suggest that MCD-aided bioaugmentation by Paracoccus sp. strain HPD-2 may be a promising practical bioremediation strategy for aged PAH-contaminated soils.

Variation of soil enzyme activity and microbial biomass in poplar plantations of different genotypes and stem spacings

To improve the productivity of poplar planta- tions, a field experiment of split-plot design with four tree spacings and three poplar clones was established, and four soil enzyme activities and microbial biomass were monitored in the trial. Soil enzyme activities, in most cases, were significantly higher in topsoil （0-10 cm） than in lower horizons （10-20 cm）. Soil cellulase, catalase and protease activities during the growing season were higher than during the non-growing season, while invertase activity followed the opposite trend. Soil invertase, cellulase and catalase activities varied by poplar clone but soil protease activity did not. Cellulase and protease activities in the plantation at 5 × 5 m spacing were significantly higher than in the other spacings. The highest catalase activity was recorded at 6 × 6 m spacing. At the same planting density, invertase activity was greater in square spacings than in rectangular spacings. Soil microbial biomass was also significantly affected by seedling spacing and poplar clone. The mean soil MBC was significantly lower in topsoil than in the lower horizon, while MBN showed the opposite pattern. Significantly positive correlations were observed among soil cellulase, protease and catalase activities （p 〈0.01）, whereas soil invertase activity was negatively and significantly correlated with cellulase, protease and catalase activities （p 〈 0.01）. Soil microbial biomass and enzyme activities were not correlated except for a significantly negative correlation between soil MBC and catalase activities. Variations in soil enzyme activity and microbial biomass in different poplar plantations suggest that genotype and planting spacing should be considered when modeling soil nutrient dynamics and managing for long-term site productivity.

Dissipation of polycyclic aromatic hydrocarbons and microbial activity in a field soil planted with perennial ryegrass

Dissipation and plant uptake of polycyclic aromatic hydrocarbons （PAHs） in contaminated agricul- tural soil planted with perennial ryegrass were investigated in a field experiment. After two seasons of grass cultivation the mean concentration of 12 PAHs in soil decreased by 23.4% compared with the initial soil. The 3-, 4-, 5-, and 6- ring PAHs were dissipated by 30.9%, 25.5%, 21.2%, and 16.3% from the soil, respectively. Ryegrass shoots accumulated about 280 ug.kg1, shoot dry matter biomass reached 2.48 x 104kg-ha1, and plant uptake accounted for about 0.99% of the decrease in PAHs in the soil. Significantly higher soil enzyme activities and microbial community functional diversity were observed in planted soil than that in the unplanted control. The results suggest that planting ryegrass may promote the dissipation of PAHs in long-term contaminated agricultural soil, and plant-promoted microbial degradation may be a main mechanism of phytoremediation.

Characteristics and Influencing Factors of the Microbial Concentration and Activity in Atmospheric Aerosols over the South China Sea

Oceans are important sources of microbes in atmospheric aerosols;however, information about the characteristics of airborne microbes and their influencing factors over oceans is lacking. Here we report the characteristics of the microbial abundance and activity in aerosols sampled near the sea surface over the South China Sea(SCS) from May to June 2016. The airborne microbial concentration range in the aerosols was 1.68?105 to 4.84?105 cells m-3 over the SCS, reflecting an average decrease of 40% – 54% over the SCS compared with that in the samples from the coastal region of Qingdao. About 63% – 76% of the airborne microbes occurred in coarse particles(> 2.1 ?m), with a variable size distribution over the SCS. The microbial activity range in aerosols, measured by the fluorescein diacetate(FDA) hydrolysis method, was 2.09 – 11.97 ng m-3 h-1 sodium fluorescein(SF) over the SCS, which was 15% – 79% lower than that over the coastal region. These values reflected a different spatial distribution over the SCS from that of the microbial concentration. Except for certain samples, all samples had 68% of the microbial activity occurring in coarse particles. Correlation analysis showed that the microbial abundance and activity were positively correlated with the aerosol, organic carbon(OC), and water-soluble organic carbon(WSOC) concentrations, indicating that the airborne microbes may be related to the reactions of certain water-soluble organic chemicals in the atmosphere. Moreover, the concentrations of airborne microbes were significantly negatively correlated with the horizontal offshore distance. The microbial concentration and activity were significantly correlated with wind speed.

Effect of Lead Contamination on Soil Microbial Activity Measured by Microcalorimetry

Microcalorimetry was used to investigate the microbial activity in three types of soil （orchard soil, crop soil, forest soil） in Wuhan, China, and to evaluate the influence of different concentrations of lead （Pb^2＋） on soil microbial activity. The experimental results revealed that due to different physical and chemical characteristics of the soils, soil microbial activity in three soil samples were in a descending sequence： orchards soil, crops soil, forest soil. Six levels ofPb viz. 0, 10, 20, 40, 80, 160 μg·g^-1 were applied in these soils, and the results showed that an in- crease of the amount of Pb^2＋ is associated with a decrease in microbial activity in the soils due to the toxic effect of Pb^2＋. In order to gain further insight of the sequential change of microorganisms, determination of colony forming units （CFU） was performed to provide a negative linear correlation between the heat effect and the respective number of microorganisms in the system.

Performance Evaluation and Microbial Shift of Sequencing Batch Biofilm Reactor Treating Synthetic Mariculture Wastewater Under Different Dissolved Oxygen at Aerobic Phase

The impact of dissolved oxygen(DO)at aerobic phase on the nitrogen removal,extracellular polymeric substances(EPS),microbial activity and microbial community of sequencing batch biofilm reactor(SBBR)have been evaluated in treating mariculture wastewater.The oxygen uptake rate and nitrification rate declined with DO concentration from 3–4 to 1–1.5mgL^(-1),whereas the denitrification rate had an increment.The activities of nitrifying enzymes reduced with the decrease of DO concentration at aerobic phase,but those of denitrifying enzymes illustrated opposite results.The nitrification and denitrification rates displayed the similar variation tendency with the relevant enzymatic activities as DO concentration decreased.The protein(PN)and polysaccharide(PS)content in EPS decreased as DO concentration declined,whereas the PN/PS ratio increased.The microbial community showed obvious difference as DO concentration decreased from 3–4 to 1–1.5mgL^(-1).The microbial co-occurrence,keystone taxa and sig-nificant difference illustrated some variations at different DO concentrations.

Soil resource availability impacts microbial response to organic carbon and inorganic nitrogen inputs

Impacts of newly added organic carbon （C） and inorganic nitrogen （N） on the microbial utilization of soil organic matter are important in determining the future C balance of terrestrial ecosystems. We examined microbial responses to cellulose and ammonium nitrate additions in three soils with very different C and N availability. These soils included an organic soil（ 14.2% total organic C, with extremely high extractable N and low labile C）, a forest soi1（4.7% total organic C, with high labile C and extremely low extractable N）, and a grassland soil（1.6% total organic C, with low extractable N and labile C）. While cellulose addition alone significantly enhanced microbial respiration and biomass C and N in the organic and grassland soils, it accelerated only the microbial respiration in the highly-N limited forest soil. These results indicated that when N was not limited, C addition enhanced soil respiration by stimulating both microbial growth and their metabolic activity, New C inputs lead to elevated C release in all three soils, and the magnitude of the enhancement was higher in the organic and grassland soils than the forest soil. The addition of cellulose plus N to the forest and grassland soils initially increased the microbial biomass and respiration rates, but decreased the rates as time progressed. Compared to cellulose addition alone, cellulose plus N additions increased the total C-released in the grassland soil, but not in the forest soil. The enhancement of total C- released induced by C and N addition was less than 50% of the added-C in the forest soil after 96 d of incubation, in contrast to 87.5% and 89.0% in the organic and grassland soils. These results indicate that indigenous soil C and N availability substantially impacts the allocation of organic C for microbial biomass growth and/or respiration, potentially regulating the turnover rates of the new organic C inputs.

Anti‑oral Microbial Flavanes from Broussonetia papyrifera Under the Guidance of Bioassay

A new favane,bropapyriferol(1),and eleven known ones were isolated from the EtOAc part of Broussonetia papyrifera under the guidance of bioassay.The structure of compound 1 was determined by extensive 1D and 2D NMR,[α]_(D) spectroscopic data and quantum computation.Daphnegiravan F(2)and 5,7,3′,4′-tetrahydroxy-3-methoxy-8,5′-diprenylfavone(3)showed signifcantly anti-oral microbial activity against fve Gram-positive strains and three Gram-negative strains in vitro.Especially,compound 3 was more potent in suppressing Actinomyces naeslundii and Porphyromonas gingivalis(MIC=1.95 ppm)than the positive control,triclosan.

Changes of soil microbial communities during decomposition of straw residues under different land uses

Monitoring soil microbial communities can lead to better understanding of the transformation processes of organic carbon in soil. The present study investigated the changes of soil microbial communities during straw decomposition in three fields, i.e., cropland, peach orchard and vineyard. Straw decomposition was monitored for 360 d using a mesh-bag method. Soil microbial metabolic activity and functional diversity were measured using the Biolog-Eco system. In all three fields, dried straws with a smaller size decomposed faster than their fresh counterparts that had a larger size. Dried corn straw decomposed slower than dried soybean straw in the early and middle stages, while the reverse trend was found in the late stage. The cropland showed the highest increase in microbial metabolic activity during the straw decomposition, whereas the peach orchard showed the lowest. There was no significant change in the species dominance or evenness of soil microbial communities during the straw decomposition. However, the species richness fluctuated significantly, with the peach orchard showing the highest richness and the cropland the lowest. With different carbon sources, the peach orchard utilised carbon the most, followed by the cropland and the vineyard. In all three fields, carbon was utilized in following decreasing order： saccharides〉amino acids〉polymers〉polyamines〉carboxylic acids〉aromatic compounds. In terms of carbon-source utilization, soil microbial communities in the peach orchard were less stable than those in the cropland. The metabolic activity and species dominance of soil microbial communities were negatively correlated with the straw residual percentage. Refractory components were primarily accumulated in the late stages, thus slowing down the straw decomposition. The results showed that dried and crushed corn straw was better for application in long-term fields. The diversity of soil microbial communities was more stable in cropland than in orchards during the straw decomposition.

Impact of fluxapyroxad on the microbial community structure and functional diversity in the silty-loam soil

The aim of this work was to assess the effect of applying three different doses of fluxapyroxad on microbial activity, community structure and functional diversity as measured by respiration, microbial biomass C, phospholipid fatty acid （PLFA） and community-level physiological profiles （CLPPs）. Our results demonstrated that substrate-induced respiration （on day 15） and microbial biomass C （on days 7 and 15） were inhibited by fiuxapyroxad, but stimulation was observed thereafter. In contrast, fluxapyroxad addition increased the basal respiration and metabolic quotients （qCO2） and respiratory quotients （QR）. Analysis of the PLFA profiles revealed that the total and bacterial biomass （both Gram-positive bacteria （GP） and Gram-negative bacteria （GN）） were decreased within the initial 15 days, whereas those as well as the GN/GP ratio were increased at days 30 and 60. Fluxapyroxad input decreased the fungi biomass but increased the bacteria/fungi ratio at all incubation time. Moreover, high fluxapyroxad input （75 mg fluxapyroxad kg-1 soil dry weight） increased the microbial stress level. A principal component analysis （PCA） of the PLFAs revealed that fluxapyroxad treatment significantly shifted the microbial community structure, but all of the observed effects were transient. Biolog results showed that average well color development （AWCD） and functional diversity index （H′） were increased only on day 60. In addition, the dissipation of fluxa- pyroxad was slow in soil, and the degradation half-lives varied from 158 to 385 days depending on the concentration tested.

Relationship between Microbial Community Characteristics and Flooding Efficiency in Microbial Enhanced Oil Recovery

Microbial enhanced oil recovery (MEOR) is the research focus in the field of energy development as an environmentally friendly and low cost technology. MEOR can bes divided into indigenous microbial oil recovery and exogenous microbial oil recovery. The ultimate goal of indigenous microbial flooding is to enhance oil recovery via stimulation of specific indigenous microorganisms by injecting optimal nutrients. For studying the specific rule to activate the indigenous community during the long-term injection period, a series of indigenous displacement flooding experiments were carried out by using the long-core physical simulation test. The experimental results have shown that the movement of nutrients components (i.e., carbon/nitrogen/phosphorus) differed from the consumption of them. Moreover, there was a positive relationship between the nutrients concentration and bacteria concentration once observed in the produced fluid. And the trend of concentration of acetic acid was consistent with that of methanogens. When adding same activators, the impacts of selective activators to stimulate the indigenous microorganisms became worse along with the injection period, which led to less oil recovery efficiency.

Thinning intensity affects microbial functional diversity and enzymatic activities associated with litter decomposition in a Chinese fir plantation

Microbial functional diversity and enzymatic activities are critical to maintaining material circulation during litter decomposition in forests.Thinning,an important and widely used silvicultural treatment,changes the microclimate and promotes forest renewal.However,how thinning affects microbial functional diversity and enzymatic activities during litter decomposition remains poorly understood.We conducted thinning treatments in a Chinese fir plantation in a subtropical region of China with four levels of tree stem removal（0,30,50,and 70%）,each with three replicates,and the effects of thinning on microbial functional diversity and enzymatic activities were studied 7 years after treatment by collecting litter samples four times over a 1-year period.Microbial functional diversity and enzymatic activities were analyzed using Biolog Ecoplates（Biolog Inc.,Hayward,CA,USA）based on the utilization of 31 carbon substrates.Total microbial abundance during litter decomposition was lower after the thinning treatments than without thinning.Microbial functional diversity did not differ significantly during litter decomposition,but the types of microbial carbon-source utilization did differ significantly with the thinning treatments.Microbial cellulase and invertase activities during litter decomposition were significantly higher under the thinning treatments due to changes in the litter carbon concentration and the ratios of carbon and lignin to nitrogen.The present study demonstrated the important influence of thinning on microbial activities during litter decomposition.Moderate-intensity thinning may maximize vegetation diversity and,in turn,increase the available substrate sources for microbial organisms in litter and promote nutrient cycling in forest ecosystems.

Effects of butachlor on microbial enzyme activities in paddy soil

This paper reports the influences of the herbicide butachlor( n butoxymethl chloro 2', 6' diethylacetnilide) on microbial respiration, nitrogen fixation and nitrification, and on the activities of dehydrogenase and hydrogen peroxidase in paddy soil. The results showed that after application of butachlor with concentrations of 5.5 μg/g dried soil, 11.0 μg/g dried soil and 22.0 μg/g dried soil, the application of butachlor enhanced the activity of dehydrogenase at increasing concentrations. The soil dehydrogenase showed the highest activity on the 16th day after application of 22.0 μg/g dried soil of butachlor. The hydrogen peroxidase could be stimulated by butachlor. The soil respiration was depressed within a period from several days to more than 20 days, depending on concentrations of butachlor applied. Both the nitrogen fixation and nitrification were stimulated in the beginning but reduced greatly afterwards in paddy soil.

Microbial community structure and functional metabolic diversity are associated with organic carbon availability in an agricultural soil

Exploration of soil environmental characteristics governing soil microbial community structure and activity may improve our understanding of biogeochemical processes and soil quality. The impact of soil environmental characteristics especially organic carbon availability after 15-yr different organic and inorganic fertilizer inputs on soil bacterial community structure and functional metabolic diversity of soil microbial communities were evaluated in a 15-yr fertilizer experiment in Changping County, Beijing, China. The experiment was a wheat-maize rotation system which was established in 1991 including four different fertilizer treatments. These treatments included： a non-amended control（CK）, a commonly used application rate of inorganic fertilizer treatment（NPK）; a commonly used application rate of inorganic fertilizer with swine manure incorporated treatment（NPKM）, and a commonly used application rate of inorganic fertilizer with maize straw incorporated treatment（NPKS）. Denaturing gradient gel electrophoresis（DGGE） of the 16 S r RNA gene was used to determine the bacterial community structure and single carbon source utilization profiles were determined to characterize the microbial community functional metabolic diversity of different fertilizer treatments using Biolog Eco plates. The results indicated that long-term fertilized treatments significantly increased soil bacterial community structure compared to CK. The use of inorganic fertilizer with organic amendments incorporated for long term（NPKM, NPKS） significantly promoted soil bacterial structure than the application of inorganic fertilizer only（NPK）, and NPKM treatment was the most important driver for increases in the soil microbial community richness（S） and structural diversity（H）. Overall utilization of carbon sources by soil microbial communities（average well color development, AWCD） and microbial substrate utilization diversity and evenness indices（H＇ and E） indicated that long-term inorganic fertilizer with organic amendments incorporated（NPKM, NPKS） could significantly stimulate soil microbial metabolic activity and functional diversity relative to CK, while no differences of them were found between NPKS and NPK treatments. Principal component analysis（PCA） based on carbon source utilization profiles also showed significant separation of soil microbial community under long-term fertilization regimes and NPKM treatment was significantly separated from the other three treatments primarily according to the higher microbial utilization of carbohydrates, carboxylic acids, polymers, phenolic compounds, and amino acid, while higher utilization of amines/amides differed soil microbial community in NPKS treatment from those in the other three treatments. Redundancy analysis（RDA） indicated that soil organic carbon（SOC） availability, especially soil microbial biomass carbon（Cmic） and Cmic/SOC ratio are the key factors of soil environmental characteristics contributing to the increase of both soil microbial community structure and functional metabolic diversity in the long-term fertilization trial. Our results showed that long-term inorganic fertilizer and swine manure application could significantly improve soil bacterial community structure and soil microbial metabolic activity through the increases in SOC availability, which could provide insights into the sustainable management of China＇s soil resource.

Foliar Dicamba Application Has No Lasting Effects on Microbial Activities in the Soybean Rhizosphere

The proliferation of glyphosate-resistant weeds has resulted in significant losses in the productivity of crops such as corn, soybean, and cotton. As a result, new crop varieties with resistance genes from other herbicides, such as 2,4-D and dicamba, have been developed as part of alternative weed control cropping systems. However, little is known about how the application of these herbicides impacts the microorganisms that carry out nutrient cycling in the soil of these cropping systems, particularly in the rhizosphere, the soil compartment immediately adjacent to the root system which is pivotal to plant nutrient uptake. The purpose of the current study was to assess the effects of dicamba on soil enzyme activities linked to C, N, and P cycling in the rhizosphere of resistant soybean plants. While dicamba had no significant effects on the activities of enzymes linked to C or P cycling in the rhizosphere, N-acetylglucosaminidase activity was temporarily inhibited, but recovered by three days after application. These results suggest there are no long-lasting negative effects of dicamba in the rhizosphere of treated plants when applied at field rates.

Microbial Processes in Stratified Lake Doroninskoe(Transbaikal Region)

In recent decades,meromictic ponds attract the attention of researchers in different directions,because here the character of the physical,chemical and biological processes differ from those of typical mixing waters(Kuznetsov,1970;Hutchinson,1969).In Transbaikalia widely distributed soda and salt lakes with different salinity.Notable among them is Lake Doroninskoye,which has a pronounced stratification for a

Linkages between soil microbial stability and carbon storage in the active layer under permafrost degradation

The Qinghai-Tibet Plateau(QTP)distributes the largest extent of high-altitude mountain permafrost in the world(Zou et al.,2017),which has different characteristics from high-latitude permafrost(Yang et al.,2010)and stores massive soil carbon.